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DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex

Sarah Schaack1*, Eunjin Choi2, Michael Lynch2 and Ellen J Pritham1

Author Affiliations

1 Department of Biology, University of Texas-Arlington, 501 S. Nedderman Drive, Arlington, TX 76019, USA

2 Department of Biology, Indiana University, 1001 E. Third St, Bloomington, IN 47405, USA

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Genome Biology 2010, 11:R46  doi:10.1186/gb-2010-11-4-r46

Published: 30 April 2010

Additional files

Additional file 1:

Tables S1, S2, and S3. Table S1 includes the best hits based on TBLASTN for each DNA transposon family identified in the D. pulex genome. Table S2 includes rates of putative somatic gains per ancestral insertion in six families of transposable elements across mutation-accumulation lineages where sex was promoted (sexuals) and prohibited (asexuals). Table S3 contains primer sequences.

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Additional file 2:

Supplemental Data S1 and Table S4. Data S1 is a FASTA file of canonical D. pulex Class 2 DNA transposons. Table S4 lists the scaffold and coordinates for all regions of the genome masked by canonical representatives of the DNA transposons in D. pulex (note that these are not filtered based on size or similarity).

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Additional file 3:

Alignments showing conserved protein-coding regions for representatives from each major family of TE identified in the D. pulex genome (a) Tc1/mariner superfamily, (b) Pogo (subfamily of Tc1/mariner), (c) Ant (subfamily of Tc1/mariner), (d) hAT, (e) P-element, (f) Mutator, (g) PIF/Harbinger, (h) Merlin, (i) CACTA, (j) Maverick.

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Additional file 4:

Transposon display results for five DNA transposon families assayed across lineages where sex was promoted or prohibited including scoring rubric.

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Additional file 5:

Trace file from transposon display reactions showing evidence for a putative germline gain of a copy of the hATA1.1 element. The top four traces show separate runs for the sample, indicating a new, replicable peak is found at 385 bp (red box). A putative somatic insertion is also visible in the top trace file (at 436 bp; blue box) where a new peak was observed in only this replicate. The bottom two traces are from another line and represent the ancestral state for the lineages lacking these new copies.

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Additional file 6:

Peak heights for transposon display performed for hATA1.1 using MA lines of D. pulex. All peaks were above minimum thresholds for inclusion (see Additional file 4). Peaks were scored based on replicability as a: 1, ancestral insertion (common across lineages and replicable within a lineage); 2, new germline insertion (found only in one lineage, replicable in all TD reactions); or 3, putative somatic insertion (unique to one lineage and not replicable in three TD reactions). Peak heights are based on heights scored by Genemapper software for each of three TD replicate reactions performed for each lineage, with the heights for the new germline insertion shown in pink (described in Additional file 5). Lines represent a best fit for each group.

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